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Error: Bowtie2: ...does not exist or is not a Bowtie2 index

Hi,

I have created my bowtie2 indexes but they cant seem to be located when I run my code.

file=$"S1_7"
ribosomal="/lustre7/home/lustre3/mas/mm10/Sequence/AbundantSequences/musRibosomal"
singularity exec /usr/local/biotools/b/bowtie2:2.3.3.1--py36pl5.22.0_0 bowtie2 -p 6  --un-conc ${file}_noribo.fq --al-conc ${file}_ribo.fq  -x $ribosomal  -1 ${file}_R1_3.fastq -2 ${file}_R2_3.fastq

(ERR): "/lustre7/home/lustre3/mas/mm10/Sequence/AbundantSequences/musRibosomal" does not exist or is not a Bowtie 2 index
Exiting now ...

Is there anything I am doing wrong here?

Thanks in advance.

rna-seq alignment
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updated by ATpoint ATpoint • written by mas • mas

The error is pretty obvious. What is the name of the index files? Can you go into the index directory and show the output of ls?

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written by ATpoint ATpoint

Thank you, I'm completely new to this field. Here is the output of ls. musRibosomal.fa rRNA.1.bt2 rRNA.2.bt2 rRNA.3.bt2 rRNA.4.bt2 rRNA.rev.1.bt2 rRNA.rev.2.bt2

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written by mas • mas

1 answer

Use ribosomal="/lustre7/home/lustre3/mas/mm10/Sequence/AbundantSequences/musRibosomal/rRNA" indicating the basename of the index files instead of only the directory. Please also see the bowtie2 manual for further usage advice.

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written by ATpoint ATpoint

Thank you, but it still comes up with the same error.

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written by mas • mas

Can show the command and error?

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written by ATpoint ATpoint

Here is it.

file=$"S1_7"
ribosomal="/lustre7/home/lustre3/mas/mm10/Sequence/AbundantSequences/musRibosomal/rRNA"
singularity exec /usr/local/biotools/b/bowtie2:2.3.3.1--py36pl5.22.0_0 bowtie2 -p 6  --un-conc ${file}_noribo.fq --al-conc ${file}_ribo.fq  -x $ribosomal  -1 ${file}_R1_3.fastq -2 ${file}_R2_3.fastq
(ERR): "/lustre7/home/lustre3/mas/mm10/Sequence/AbundantSequences/musRibosomal/rRNA" does not exist or is not a Bowtie 2 index
Exiting now ...
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updated by ATpoint ATpoint • written by mas • mas

Something wrong with the index then, how did you generate it (command)?

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written by ATpoint ATpoint

Here is the command to generate the index.

singularity exec /usr/local/biotools/b/bowtie2:2.3.3.1--py36pl5.22.0_0 bowtie2-build musRibosomal.fa rRNA

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written by mas • mas

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